Currently there’s not a great way to recover from such corruption, other than migrating to a new repository.
You need to create second repository and use kopia snapshot migrate. To make sure you’re not mixing those up, always pass --config-file:
kopia --config-file /path/to/new.config repository create ...
kopia --config-file /path/to/new.config snapshot migrate --source-config /path/to/old.config
kopia --config-file /path/to/old.config repository disconnect
This will copy snapshot from a corrupted repository to a clean ones - any invalid files due to unreadable chunks will be treated the same way as if there were bad sectors/read errors on the original disk - they will be reported as errors and ignored, so you will end up with a clean repository that’s missing some files.